Ghost Protocol
by MBHHCP-PR-19
Summary: TEMPORARY HIATUS ( ... Activating this protocol will leave you without support, or back-up. Activating this protocol is considered suicide, especially if you're caught. AN: I don't know how this is gonna go but I do tend to have some violence when writing. Sexual content is a possibility but not guaranteed. Main characters included, possible Avengers sightings here and there.
1. Chapter 1

_**Ghost Protocol**_

_Activating this protocol will leave you without support, or back-up. _

_Activating this protocol is considered suicide, especially if you're caught._

**Disclaimer: I own nothing that is claimed by Marvel. **

**I do own a couple of later characters and this plot.**

"Yo, A.C?" Skye called over comms. "Three inbound on your six!"

"Copy!" came the reply as she watched him duck into a vacant room. She trained her eyes on the three figures as they made their way through the corridors, following Coulson's path. When they slowed to a stop outside the room where her boss was, she felt her heart leap into her throat, "A.C!"

The last thing she saw was the smallest of the three, female, reach for the door before her feeds went down. She screamed through comms hoping for a response, tried accessing the cameras, audio, anything. Nothing worked. Less than a minute later, Fitzsimmons and May rushed in, "Skye? What happe..." Noticing the blank screens, they trailed off and she saw all three pale, May slightly. "He shouldn't have gone in alone! _He shouldn't have gone in alone!" _Skye launched her headset at the central screen and all but sprinted to the armoury, the older agent hot on her heels.

Arming themselves to the eyeballs in record time, they grabbed extra ammunition just in case. Combat knives sheathed and in boots. Sidearm's, Glock 17's at their hips. Assault rifles in hand, the M4A1 Carbine. Fitzsimmons having caught up produced custom made grenade belts which both women slung overhead, looping one arm through.

They'd parked the 'bus' in a small-ish field about a mile from the compound. So, with Skye on point and May bringing up the rear, they headed to the compound through a large patch of mildly dense trees, gunfire getting louder with every step. May hated guns, preferring hand-to-hand combat instead, but they'd found this compound practically oozing HYDRA agents so she had no other choice. She wasn't going to unleash 'The Cavalry,' it wasn't her anymore.

As the building came into view, both women sped up and stopped at a small cluster of trees, adequate shelter. Coulson and two others were sandwiched between two MDX's, brandishing the HYDRA signature. Shells were raining down on them from all directions.

The women stood, knees slightly bent, weapons raised and turned to look at each other. Calming themselves, they wore their war faces, void of emotion and nodded. Skye moving to the left, May to the right, stepping forward in unison and opening fire.

HYDRA agents scattered or dropped. A few seconds later, May found herself dodging a rogue arrow and opened fire again. Coulson and co turned, recognition claiming their faces as the women stepped out of the shadows of the trees raining a hail of gunfire down on the enemy. Coulson's heart swelled with pride but he didn't let it show. He watched as the women, creeping forward still, hit the magazine release, reloaded and opened fire for the third time.

May caught Coulson's eyes and gestured with her head for them to move out. As she lay down the necessary cover fire, she caught Skye pulling the belt off in her periphery and followed suit. Seconds apart, buttons were pushed and belts were launched.

The women retreated to the trees, covering the group, scanning their surroundings for stragglers until the almost perfectly timed explosions. They ran to catch up, dodging trees, still observing, covering, focused.

Finally making it to the 'bus,' they relaxed slightly and May took off for the cockpit immediately after depositing her weaponry in the lab. Thinking they were safe, Skye scanned the area and turned as the shot rang out. Delayed reaction caught her as still as a statue until the darkness broke out.

The wind picked up around them, her hair flailing wildly and her eyes. God, her eyes were blood red with feline-like pupils as black as the darkest shadows. Skin, a sickly shade of white, showing black veins. Palms facing forward, stalk still, she hovered a few inches above the solidity that was the hold floor.

The wind had gotten worse with every passing second. "Skye?!" Coulson and Fitzsimmons enquired. One of their guests stood, jaw on the floor, eyes wide. The other, smirked and stood in front of her.

"Hey, Angel! Get your pretty little ass down here or I'll have your precious birdie hit you with a tranq!" The woman waited, watching, looking bored. When it finally seemed like she was calming down, a lack of almost hurricane-like winds, Coulson told their guests to meet him in the briefing room and continued to watch as his girl reined her emotions in. If he didn't view her as the closest thing to a daughter that he had, she'd have gone on the Index and would have a different commanding officer. But she was family and you don't turn your back on family, no matter what!

When she'd finally gone back to her usual self, she could barely breathe, the air coming and going in short, fast puffs. She shuffled towards the lab, removing her t-shirt as quickly and as painlessly as possible. Coulson let out a long breath when he saw that she'd worn the skin-tight bullet proof vest shirt but turned away as she proceeded to remove it. When he turned back, she was lifting one side of a bright purple sports bra, sitting awkwardly on the examination table. That's when he noticed the black bruise working its way up her rib cage, round her back, across her front and down towards her hips. She'd be in pain for a while.

The vests were designed to stop the bullets from penetrating the skin but that didn't stop the damage done from the force. Yes, she had heightened healing capabilities but it'd still take a few days for the pain to subside.

"Orders, Skye. Orders are to be followed! It's not that I'm not grateful, but you could have gotten yourselves killed and I'd need to find a new number two! _What the hell were you thinking?!_" Coulson was almost shouting and Skye, glaring at him.

Slowly gaining the ability to breathe normally, she replied, "Director Coulson, _sir_, I don't give a damn about orders! Do you expect me to step up when you've been cut down? Do you expect me to just take on all that responsibility? Do you expect me to leave the only father I've ever known to die in enemy hands? No, I'm not just an Agent of SHIELD. No, I'm not some ops robot. No, I'm not gonna stand back and let the only father figure I've ever known commit suicide by hostiles. If you wanted someone like that, you should've made May or Hill your second, but you're welcome, _sir!_" She'd let her feelings known to all, and she watched as the silent blush spread like wildfire up his face. Smirking, she stalked off to her bunk and collapsed on her bed. She'd never been this exhausted in a while. In all fairness, it'd been a while since she'd let her origins out. Her 0-8-4 status was only known to those closest to her and she'd never let herself unleash it in front of someone other than family before.

For once in her life, her dreams were peaceful. No biological father being a completely manipulative moron. No bodies littering the walkway she'd casually strolled along. No Grant threatening to take her out. No Jemma jumping from the cargo hold. No Fitz being in a coma. No Coulson shouting, begging for death. No May, silent tears staining her cheeks. Honestly, the last one frightened her more than anything else. She'd never seen May so emotional and the people person in her didn't know what to do. She wanted to hug, to comfort the older woman but the fear of having her head virtually torn off held her back. She'd never seen her mother, for all intents and purposes, look so vulnerable and yet, so strong. She'd studied May, the way her shoulders shook, sobs threatening to tear through her chest. Studying the way the strongest woman she'd known fell apart. At that point in time, she didn't care. She didn't care if the woman rejected her comfort, didn't care if the woman physically removed the arm from her body, and didn't care if anyone saw what was going on because she needed the woman to know that she was there. That she would always be there, any time, any place, as long as it didn't blow her cover!

She slept the entire night, through dinner, through Tai Chi, breakfast and lunch. Using that side of her, the side she loved to hate, drained her energy because she didn't use it often enough. She'd pushed it away for too long and it was starting to show more and more and if she didn't get it under control, she knew they'd have to put her down eventually.


	2. Chapter 2

_**Ghost Protocol**_

_Activating this protocol will leave you without support, or back-up._

_Activating this protocol is considered suicide, especially if you're caught._

**Disclaimer: I own nothing that is claimed by Marvel.**

**I do own a couple of later characters and this plot.**

When she got up, after her morning hygiene routine, she went straight to the cargo hold for a workout. Putting her headphones in, cranking the volume up and wrapping her hands, she let the plan come together. Pounding away at the bag, ducking, dodging air, she felt eyes on her. The hair on the back of her neck stood on end but she carried on. Finally feeling tired enough; she unwrapped her hands and stretched, cooling down. Grabbing a bottle of water, she made her way to the kitchen. She didn't expect it, she didn't see it coming and she almost choked.

_Him._ HYDRA Agent, Grant Ward.

She kept her face neutral and headed for the kitchenette completely ignoring him for sandwiches! She didn't hear a thing except her music. Had she turned her music off, she'd have heard him asking Fitzsimmons who she was. Cutting the tomatoes and cucumber with a very sharp knife, she felt a hand on her shoulder. Instinct kicked in and she had Agent Clint Barton pinned, blade at his throat within seconds.

"Oh. My. God!" she screamed. With Barton flinching at the unreasonably high pitched screech from her, she backed off, pulled a bud and helped him, "Sorry Birdie, I had no idea you were here! Why didn't you tell me?" Setting the knife aside, she rushed at him, arms wide.

"Don't worry about it Demon, I should've known better! I forgot Coulson had Nat and Mel train you. Only the best for his second, ya know? And you were sleeping, wasn't going to disturb you," Clint returned the hug. Pulling away and holding her at arm's length, "I see you've a few new scars. What in the _hell _is that?!" He turned her to get a better look at the once black bruise across her ribcage, now purple. She shrugged and turned back to sandwich making.

"It's nothing C.B, rogue bullet. Had my vest on. Be all healed up in a few days, then I can kick your ass. Kosher!" Slapping on the top slice of bread, cutting into triangles, she bit into it and gave a moan of satisfaction. Natasha chose that moment to stroll in, smirking.

"So, it was you three I saw on cam? Way to give a girl a heart attack! I thought A.C was a goner," she turned to Clint. "I didn't see you between the MDX's," and then it dawned on her. "You fired the arrow at May! We got half chimp, half hawk here or what?" She tried to keep a straight face, she really did, but she ended up doubled over, laughing hard! When she was finally able to regain her composure, "man, I gotta tell Fitz. He'd have a field day with you!"

"I suspect you've met our latest recruit? Anything to say about that?" That was so Nat. Always straight to the point, no sugar coating and Skye really liked sugar!

The facial expression said it all, she was livid among other things but she couldn't form the necessary words politely.

"Natasha, Clint, a word please?" Coulson had been watching the exchange, he'd enjoyed watching as they'd gotten to know one another. As he headed up to his office, both agents following, Skye replaced her headphones and went back to the cargo hold.

On passing the lab, she saw Simmons make a beeline for her and turned in that direction. She didn't see the other agent standing above, watching her every move.

"So, what's up?" she asked as the older but much younger looking agent pulled her into the lab.

"Ward! He doesn't know who we are. He doesn't know who you are. He knows nothing about his affiliation with HYDRA. He knows his work as a specialist but other than that, he doesn't have the slightest idea about who he is. I mean, with everything that's going on related to HYDRA, you'd think he knew something, anything to help. Goodness, I'm blabbering again, aren't I? Fitz, help?" the young scientists looked flustered, annoyed but relieved.

"Well, we asked him about-"

"-his family and Agent-"

"-Garret and he doesn't-"

"-know a thing about the guy. It's as if-"

"-he's had his memory-"

"-wiped and the only people we know with those-"

"-capabilities has gone off the grid. We can't find them anywhere, but-"

"-it's Fury. The guy's a ghost when he wants to be. How are we-"

"-supposed to handle this? Just forgive him and-"

"-get on with it?" Skye couldn't help but think they were two of the most adorable people on Earth. Sure, they were in a relationship, thanks to Ward but they'd never forgotten _how_ it happened.

"I'm gonna go work out, I'm really not in the mood for this type of discussion. I'd kill him if Coulson wouldn't hang me for it but that's just me!" as she slowly retreated, still facing them, she hit something solid that wasn't glass. She turned slowly and almost, _almost_, lost her cool.

"Agent Grant Ward. Who, and more to the point, what are you?" his face was expression less, much like the first few weeks they'd been on the bus together. _Typical robot,_ she thought.

"Oh, I know fine well who you are, _Agent Ward!_ The question is, why are you here?" her face stoic, showing a slight irritation.

"That's on a need to know basis, Level Eight and above. I'll ask again, who are you?" Skye had never laughed so hard in her life. Fitzsimmons were crying, Fitz on the floor trying to catch his breath. Simmons was holding on to a counter top, trying to keep her balance.

When all laughing was over and they'd finally seen Ward's extremely confused expression. "Level Eight? My identity and origins are none of your concern but next time you speak to a superior like that, you'll find yourself leaving this plane, midflight!" She'd snapped.

"You're speaking to the Deputy Director, Agent Ward!"

"_Jesus,_ Spidey! A little warning next time?! I really should start calling you Ninja, sneaking up on people like that. I almost died there."

"With all due respect Agent Romanoff, I don't believe you. No-one on this plane acknowledges rank. They make fun of each other, prank each other. Nothing about this is professional," he turned to Skye. "You're careless, unobservant, annoying and loud."

Inside, the fire was raging but, a smirk playing at her lips, "So, you'll speak to Agent Romanoff respectfully but not the Deputy Director? Agent, detain him. I'll be in the Cage soon!" and with that, she made her way to Coulson's office. Barging in, she started pacing.

"Why? Why is he here? What happened to him? Why doesn't he know me, us? What's his purpose? Why isn't he locked up? I can't do this A.C. Not with him on board, and just so you know, he's in the interrogation room...What? Don't look at me like that. He disrespected his superior and he needs to know that it's unacceptable...Again with the looks, I'd do the same to anyone else. Excluding the people who know me personally and yes, technically he knows me personally but what's with the mind voodoo? Will he remember? He's back to being the T-1000? What did Fury do to him?" she kept on with her rambling until Coulson cut her off.

"He's been in that cell for over an hour. At this moment in time, all I know is that Fury swapped out Garrett and HYDRA for him and SHIELD. With the technology upgrades in recent years, it was difficult but not impossible. Look at what Fury was able to accomplish with me but no, he doesn't remember and let's hope he never does because we know it didn't end well the last time someone's memories were messed with." Running a hand through his hair, he continued, "He's here because he's the best, besides you and May, excluding Avengers. You _can _do this! I know you can. You're strong and stubborn and loud and you're you! Now, let's show him what happens when he doesn't respect his superiors."

They gathered an audience as they headed to the interrogation room, "everyone stay outside please. I think it's time he learned just how scary I can be!" Failing to contain the devious smile, the others shared a knowing look. That was the look that told them that he'd be lucky if he didn't have nightmares for the rest of his life. Barton handed over two files, one of which was quite large.

Throwing the door open, she stepped inside and let the wind close it.

"Agent Grant Ward. You know why you're here? Care to explain why you think it's acceptable to disrespect your superiors when they're present?" No emotion on either of their faces until he didn't answer. She let the mask slip just a tiny bit, her eyes bright pink.

"I won't ask again, Agent Ward!"

"I don't need to disclose that information. As I told you earlier, everything to do with my task is Level Eight and above. Now, you tell me something. _What_ are you?" Stubborn, stubborn man! She sat his credentials in front of him and let him look them over.

"As I clearly stated earlier, my origins are none of your concern, Level Ten and above. You were saying, _Level Eight Agent Ward_?" Keeping her voice monotonous, she let the mask slip that little bit further, her eyes turned to a bright red and her pupils darkened. "About your lack of respect for women, other than Agent Romanoff, who outrank you?" Coulson stepped inside and shook his head, looking her straight in the eyes.

"Deputy Director Skye, you have a phone call. Sounds urgent and they won't speak to me." Ward turned to Coulson, obviously puzzled at how the older man address the woman. "Yes Grant, she looks, sounds and acts so much younger but here," sliding her file across the table, "are her credentials. She rebuilt SHIELD's mainframe on her own within a couple of weeks and she is more than qualified. Bit of advice? Don't call her ma'am unless you want to die. Don't annoy her, at all, unless you want to die! I've seen what she can do and it's not for the faint hearted, believe me."

Meanwhile, in the soundproofed bunk that was hers, Skye picked up the phone, "Deputy Director Skye, and you are?"

"I'm in!" She heard the _click_

Ten minutes later, another phone call came with the same phrase. The rest came shortly after, a mixture of 'I'm in' or 'Time to think.' She'd had Fitz make sure a random number of phones were untraceable and installed her own encryption data on all of them. Hers was programmed with the other numbers. The others only had hers. _Let the games begin!_


	3. Chapter 3

_**Ghost Protocol**_

_Activating this protocol will leave you without support, or back-up._

_Activating this protocol is considered suicide, especially if you're caught._

**Disclaimer: I own nothing that is claimed by Marvel.**

**I do own a couple of later characters and this plot.**

She'd given them a week and a half to think about the decision and so, using her encrypted phone, she sent the text message to every phone Fitz had gotten for her.

_I need to know, NOW!_

-A week later and she was avoiding her team like the plague. A week later and she had finally started using her heritage to her advantage. A week later and she'd decided she'd had enough. She'd watched as everyone except Fitzsimmons left for their usual supply run. She'd stood in the shadows observing as Fitzsimmons slunk away to Fitz' bunk when they thought she was in hers, and that's when she made the decision.

Typing away on the SHIELD issued laptop, she'd done it. She'd made her files above the clearance of everyone on the plane, with the exception of Coulson because he's the highest they go. It wouldn't make a difference right enough. She'd set the timer for a few hours ahead, when they'd be in the air everyone would be in the briefing room for their next case. She packed up what she needed, looking around her bunk one last time, touching the pictures on her wall lovingly and with a sigh, she departed.

Hotwiring wasn't easy, but she was glad she'd picked up the remote hotwiring device on her way through the lab, the 'Hi-Jack!' They'd parked the 'bus' in an out-of-the-way field south by south-west of Madison, Maine and she didn't have much time but she had to get away. And so, the first car she came across was her way out. She knew where she was going but she had to take the indirect route and she had to be as inconspicuous as possible. She disabled the GPS in her phone, the vehicle, a black Ford Ranger with a couple of hay bales in the bed of the truck and finally, the SHIELD issued tracking device that was embedded in the bone of her left arm. Once that was all done, she hunted down every file she had to, every signal from every tracking device they'd be carrying and disabled them. She set up an encryption to get into them, one that Fitz wouldn't be able to break through. SHIELD would be in a panic, twenty-six of their agent's offline and underground, it wouldn't be a pretty sight.

The new SHIELD valued every loyal agent they could get their hands on and as part of the signing up, on passing through their selected fields, they had to be fitted with tracking devices. In no way does it violate the privacy of the agents, it's a failsafe in case of emergencies like before they were mandatory.

_Agents Diaz and Hernandez were on an undercover op and their cover was blown. They were in their early twenties and neither had been through the level of torture they'd had to endure when they were caught, and they did have back up. Hernandez was always the stronger of the two and because of that, she'd endured a lot more than Diaz. It took two weeks to catch up with them and what the medics saw, horrified them._

_Diaz had multiple broken ribs, both arms were broken in multiple places, his right knee cap was shattered, his left femur broken in three places, left eye socket crumbling away, nose broken and out of line, two of his spinal vertebrae were fractured putting pressure on his spine. The guy was dead, he'd spilled SHIELD secrets and his captors spilled his intestines._

_However, Hernandez had the same kind of treatment. Multiple rib fractures, punctured lung, both eye sockets crumbling, both arms and legs broken in numerous places, and her hands were the worst. When SHIELD had caught up, they found her with one hand still in a vice, one man slowly pulling the lever, tightening. The screams were enough to bring nightmares to anyone who heard them._

_The woman was practically in a body cast and the mental scars were worse. This was something she wouldn't recover from without serious help. Under Skye's orders, SHIELD had gotten her the help she needed. They'd offered early retirement and a large cash sum but she'd refused, said she was still too young to retire. After seeing the effects of that kind of torture and taking how long it took them into consideration, bone embedded tracking devices were mandatory._

She drove until she had to stop for gas and sent that all important group text message.

_Ghost Protocol is a go! Twelve hours. _42°13'43.8"N 75°35'44.5"W

**Author's Note:**** I know this one's short, but 2 absolutely sucked! I don't even know where it came from. As always, review, don't review. As the reader, that is your choice.**


	4. Chapter 4

_**Ghost Protocol**_

_Activating this protocol will leave you without support, or back-up. _

_Activating this protocol is considered suicide, especially if you're caught._

**Disclaimer: I own nothing that is claimed by Marvel. **

**I do own a couple of later characters and this plot.**

At the end of the previous day, when all supplies were packed, Coulson retired to his office, May and Barton to the cockpit, Romanoff to her makeshift bunk, Fitzsimmons to the lab and Ward to the cargo hold/gym. Sleeping, writing up reports, training, doing their own thing.

They were up bright and early the next morning and half an hour after achieving cruising altitude, the team gathered in the briefing room as Skye had predicted. She'd led them to this case, she had to. "Skye, please report to briefing room. I repeat, please report to briefing room!" Normally, Skye would already be there, laptop hooked up to the holotable. On the odd occasion, she'd come bustling through the door, laptop in hand. This time, neither occurred and Coulson started shifting nervously.

Pressing the comms button again, "Skye, get your ass to the briefing room, NOW!" Again, nothing happened. Turning to the women of the team, "Can one of you go and make sure she hasn't fallen asleep? We all know what she's like when she finds a project and after the way she's been this past we..." he trailed off as the screens came to life _of their own accord._

Skye's smiling face on every screen, '_play in three, two, one._'

_"Agents of SHIELD, as Deputy Director, I need to go off grid for a while. I've asked Commander Hill to stand in my place. Be the best you can be, never doubt yourself and always, __**always**__, keep your head held high. A.C.D.C," she giggled, "May, Barton, Romanoff, Fitzsimmons, Ward! As a friend, I'm sorry I can't be there with you. I have some unfinished business to tend to and I can't go into much detail. I don't know if or when I'll be back but please, don't try looking for me," she gave a sad smile. "I'm in capable hands and I was trained by the best, _Teaspoon, Ninjasha!_ Believe me, I wanted to say something earlier but trust me, this is better done on my own terms when you're not with me, where none of you can get hurt. I love you guys!"_

The screens went black and the klaxon started blaring, red flashing lights everywhere. The computer on repeat, _'Ghost Protocol initiated.' _That was their case, straight out the window.

They just stood, staring at the blank screens, dumbfounded, "May, Barton, get us to HQ, yesterday!" Panic seeping from his every move, his every word. Sure, she'd gone off on her own before but never had she activated her own _Ghost Protocol_.

"This is bad, Fitz, this is very bad!" Simmons couldn't say anything else; she was fighting against the tears, against the sobs that threatened to overtake her body.

An hour and a half later, they landed the bus and departed quickly. On entry to the new and improved Helicarrier, they immediately clapped their hands over their ears. Again, klaxons blaring, red lights flashing, _Ghost Protocol initiated!_

"Now, what's she done?" Coulson attempted to shout above the noise. Making their way to the observation deck, they saw agents rushing around, collected of course. Their arrival had gone unnoticed until they were standing front and centre. "Computer Specialists, SHUT. IT. DOWN. NOW!" Hill was close to frantic, and that's when everything stopped. No klaxons, no lights, no annoyingly repetitive computer voice. Just people rushing around from screen to screen, person to person.

The CS' put what they were seeing up on the big screen, "Sir, we have a problem. A big problem." The guy looked terrified. All six feet of him, shaking slightly as he said his next sentence, "TheDeputyDirectorhasgonedarksir!"

The group just stared at him, "Repeat that, slowly!"

"The Deputy Director has gone dark, sir!" he stood, waiting for Coulson to blow up, but instead, became confused when the aged man smiled. "It's scaring me, sir! I mean, no-one in their right mind would take her. No-one has the balls for that! But it doesn't sit well with me. She wouldn't activate her own _Ghost Protocol_, would she? I saw the video, we all saw the video and really, the woman has balls, bigger balls than most ops specialists. Why would she activate _GP_ on her own? She knows it's a suicide mission!" The young agent seemed to be really out of it. Yeah, he made sense but the fact that he was worried about Skye said a lot.

Fitz spoke up next, "Sk-The Deputy Director had me make sure some phones were completely untraceable and you know what she's like with encryption. Auch rubbish! I wasn't supposed to tell you that."

May, Romanoff and Barton promptly exited the deck. May headed for the ops quarters, Romanoff and Barton headed off to the gym.

"Agent Lewis? Don't worry about it. You've done nothing wrong. Unfortunately, our Deputy Director has in fact initiated her own _Ghost Protocol_." And not a moment sooner, the klaxons and lights started up again. _'Ghost Protocol initiated!'_

Rushing over to a group of CS', "What's happening now? Haven't we had enough of this?"

"It's not us, sir. Someone's in the system, activating more protocols. I can't stop it. Whoever it is, they're good, better than any of us." The young woman looked shocked.

"Pull up all tracking devices on every agent we have in the field, including bodily trackers. If she's doing what I think she's doing..." he let it hang in the air. He didn't know what to say. If she was doing what he thought she was doing, she would definitely be on her own suicide mission.

"Sir, they're all disappearing one by one!" Rrealizing that what he had said was a completely foreign and unheard of concept, he continued, "There's nothing on them anymore, their trackers are dropping like flies. No phone calls, text messages or family contact for the last twenty-four hours. They've just vanished. Gone completely dark, and the numbers are still on the rise. I mean, how do you lose _th__is_ many people in very little time? No-one's answering phones, comm lines, SHIELD frequencies. It could be another HYDRA thing, or some other secret-secret organization. I'm sure there's a good reason for it, sir but the Deputy Director was the first to go. Could she be doing this?"

Everything was made a whole lot clearer. Skye wasn't one for small surprises. When she had a plan, she went all out. Coulson rested his hand on the agents shoulder in a comforting gesture, "Agent Lewis, calm down. We all know that there's only one person in the world that could take that many people off book within minutes, because it _is_ her system. No HYDRA, no other secret organization. Just our Deputy Director being herself. We need to find her as soon as possible though. I have a really bad feeling about this!"

"Sir, there's a good number of all types of transport missing, from most bases. Reports are still coming in now." Coulson turned to the man, reading his lanyard.

"Agent McKinnon, I need details. How many? Of what? How long ago?" he let out an exasperated sigh and pulled a hand down his face. _This girl is going to be the death of us all! _"And Lewis? I need names and files on everyone who's gone dark."

Thirty-five minutes later, Coulson was still waiting when Agent Lewis came running up to him, files forgotten about, "Sir, you're not going to believe this! Agent Ward has gone dark and the rest, sir?" Coulson didn't know what to think anymore, so he waited, "They're all supers!"

**Author's Note: My apologies for taking so long. Scotland has had some pretty awesome weather. We've been staying with my parents for the last week(ish) and I've been painting fences and garden sheds all weekend lol. Great opportunity for my son to get out of the house as where we live isn't the most pleasant place to live. Anyways, I think this chapter has taken the longest so far. I was going to stick with Skye for the entirety of the fic but who doesn't love a bit of the team here and there?! A big **_**thank you**_** to ****LisaMichelle25**** for the little confidence boost after Ch.3. And you all know what to do! Read and review, read and don't review. As the reader, that is your choice. I really hope you enjoy it though!**


	5. Chapter 5

_**Ghost Protocol**_

_Is a go!_

**Disclaimer: I own nothing that is claimed by Marvel. **

**I do own a couple of later characters and this plot.**

Rendezvous Point One

During Skye's trip from the bus, she sent one more text concerning latitude and longitude.

Pulling into the car park, she waited. After an hour, she got bored. Typical Skye decided it was time for a little bit of fun. Getting into position, and comfortable, another hour went by and she seen a black SUV pull into the car park. The driver flashed the headlights twice in her vehicles direction and when there was no response, made its way to the exit.

_Now's as good a time as any! _ Taking as much air into her lungs as she could, she paused for a second and let out a high-pitched, ear-piercing scream. She saw the red glare of the brake lights and continued watching as the SUV stopped, brake pads screeching. The sound of metal being ground into metal made her physically cringe. Thirty seconds later, the driver's door flew open and the occupant stepped out, weapon raised. _Great, he's gonna shoot me on sight!_ He stalked towards the tree line with precise and noiseless steps. He'd glance to either side every few feet, weapon still trained on the tree line.

She appreciated the view; it'd been too long since she'd seen the terminator in the field. _Just a few more meters, come on._ She held her breath as he finally took the last step, right underneath her perch. Moving as quickly and as quietly as possible, she dropped down onto his back and waited for it.

And there it was! He had her pinned in a matter of seconds, forearm across her throat with a little more pressure than necessary. She couldn't keep the grin off her face, "Nice to see you too robot!"

"Deputy Director, I am so sorry." He straightened and pulled her up with him. She cupped her hand over his cheek and as expected, he let his guard down and leaned into it.

"You don't have to pretend anymore Grant. I see the way you look at the team when you think no-one's watching. I know you haven't had your memory wiped and I know that Fury's orders aren't stopping you from telling them," she dusted herself off and looked up, taking his hand in hers. "There's no use in lying to me Ward so don't make me pull rank, Fury's had me in on it from the beginning. Great acting and all! You're my personal protection detail with the occasional case, that's all anyone with the clearance knows, and just so you know, Coulson doesn't."

He stared at her, tall and stiff, surf board style. You could see the tension in his jaw, even in the dark. Snatching his hand from hers, he made a beeline for the parking lot. He couldn't deal with this; Fury hadn't told him it was her. Fury hadn't told him much of anything, except that he'd be on body-guard duty for the Deputy Director. The fact that she called him out didn't do anything good for the constant turmoil inside his head. He hadn't expected any of this, the get-out-of-jail-free card, working with his team, seeing her, pretending and the orders. He was always good at pretending, he was a specialist after all.

As she shuffled after him, she sighed. Her day couldn't get any worse. She ran from her team, her family. Twirling a strand of hair around her fingers, she reached the pick-up and turned to him. She held out an earpiece and got into her vehicle when he took it.

She didn't get it. She didn't get it at all! She'd monitored his progress through interrogation, therapy, psych evals, training again. She'd monitored everything he had done since the fall of HYDRA. He was the loose brick that was pulled and tipped the balance too far. He'd basically spilled his insides during interrogation and cracked after three weeks of intense techniques and she wasn't surprised that he lasted so long. Granted, he'd spent a couple of months unable to speak due to Melinda May and they didn't dare touch either of his hands in case he finally decided to write everything down. The most creative and soul-destroying thing they'd done, was make her play dead by tentacles. It was a stupid and snide remark that took days to perfect.

_She looked on as Coulson spoke into the phone, being updated by Ward's interrogators. Two weeks and he still hadn't cracked. _

"_Really? No, he betrayed us. Get that information by any means necessary!" and he hung up. As soon as the receiver hit the phone, her head flew up expecting bad news as she pretended not to hear half of the conversation._

"_He's giving us trouble. He refuses to open his mouth and won't write anything but _bright skies_."_

"_Just shut off the damn light and let the darkness take over!" The rage in her eyes was astonishing considering she was usually cheery._

_How hadn't he seen it before? The way he looked at her, unable to suppress the urge to smile whenever she was around. The way he watched over her in her near-death experience, the death of the fake Clairvoyant after the threat towards her. He couldn't pull the trigger when he faced her. He couldn't hurt her, intentionally, orders or not. He _loved _her. He _protected_ her._

"_And that's exactly what we're going to do!" She didn't miss the spark in his eyes or the mischievous grin that took hold of his lips. "We'll 'kill' his light! Skye, are you prepared to die for this?"_

"_What?! A.C, you better be kidding! I'm too young, and annoying, and downright adorable to die!"_

"_Skye, he loves you. You_ are_ his light!" He watched as the confusion fled and the troublemaker in her shone through._

"_This, is gonna be soooooooo fun! But to make it believable, we're gonna need lots of blood. You reckon everyone is up for donating some? And we're gonna need a fake warzone." She started drawing up plans and pulled Simmons into Coulson's office after three hours._

"_Jemma, we need help! I need to die to break him. We need blood, just get four vials from everyone and throw them all together." Simmons nodded and set about her duties claiming that it was on Coulson's order. _

_Four hours later, they found themselves outside an abandoned warehouse, seven small teams on standby. Skye had the blood sealed and in place. The teams had been briefed and Fitz had the upgraded Grumpy in the air. _

_By the end of the mock fight, a supposed HYDRA soldier had Skye on her knees with her hands behind her head. She pushed the small needle into the back of her neck, waiting for the effects to take hold. Grumpy couldn't see their faces and Fitz hit the buttons as the agent pulled the trigger, blanks of course, aimed at her chest, "Hail HYDRA!" With the small outward explosions tearing her clothes apart, Skye slumped forward and as Coulson had told them to; their pretend enemies were hit with ICERs. Perfect execution, Coulson sprinted forward and turned Skye over, head and shoulders in his lap. _

_She smiled up at him, blood staining her teeth, "Did we get them A.C?"_

"_Shut up Skye. WE NEED A MED EVAC! Save your energy until the med team gets here." The memories flashed through his mind, of her covered in blood, deathly pale, dying. He felt his eyes sting and her hand on his cheek._

"_Don't A.C! Don't cry, we got them. Too bad there's no...miracle drug around." She took a breath and started coughing, blood pouring out of her mouth and down her chin. When the coughing subsided, she let her hand drop, "Look after them, Phil. They're gonna need you!" She took her 'last' breath and as the drug finally kicked in, she went limp. He let the memories consume him and he really started panicking. The sting gave way and he let the tears fall, "SKYE!" So much blood, too much blood. He started chest compressions and gave up when Simmons pulled him back, tears falling from her eyes, sobs wracking her body._

"_There's nothing we can do. There's nothing we can do." And that's when Fitz cut the feed. Some of the agents brought a gurney over and lifted Skye onto it, securing her. She'd wake up in a few hours but she'd begged Coulson not to show him the video until she was awake. When they got back to base, they waited the two and a half hours until she was on her feet._

_She watched the screen as Coulson grimly entered the room. Ward looked up at him, confused, "Sir! What happened?" Phil hadn't changed out of his bloody clothes. He hit play and slid the tablet across the table. With his head in his hands, the Director started crying, sobbing loudly. No-one knew whether it was that he actually believed he'd lost her or not, but it had done the trick. Ward sat still, the only movement was from his shoulders, his breathing was too fast._

_He looked to the camera, "Let me out! You need to let me out! Let me out! I'll kill them all! Let me out! Let me out! LET ME OUT!" The shout had brought Coulson out of his mind and he stared at the broken man before him. Grant's face was beet red, tear stricken, and his eyes held the most dangerous rage Coulson had ever seen._

_Skye hadn't been prepared for either of them crying. No-one had been prepared for it. It wasn't even remotely close to what they'd been expecting. Skye, more than anyone, had been expecting a laugh. She broke him. He was already broken, but she demolished the remains. After giving up the intel, Fury swooped in and took him away. They thought he was going to prison but apparently not._

"Agent Ward? Secure the area, they've just figured out some details of my plan and I need to throw them off. Ghost Protocol is a pain in my ass already!" He done as he was told, moving around the area making sure there were no threats.

She got another fifteen offline and heard it before she saw it, helicopter inbound. She dashed to the tree line and watched as two figures rappelled and landed. Cursing under her breath, she waited as the gear was lowered to the ground. The chopper dropped the lines and turned, heading back in the direction it came. She could distinctly hear the accents carrying over in the wind.

"What are you two doing here? And wow, when did you learn to rappel like that? Wait, it was Coulson's training, wasn't it? Oh God, Grant's gonna kill me!" She stepped out of the shadows and stormed forward. Hugging both, she handed them their comm links.

"Well," Fitz rubbed the back of his neck, "I kind of kept a phone, just in case. And it's a good thing I did, because if I didn't, I wouldn't be able to kick Ward's ass for lying to us." He turned to the man, "We know, Ward. The damn thing was supposed to float. You gave us a chance after the order to execute us. You went against Garrett and you gave us a chance. I don't know how hard that was for you but if you hadn't, we wouldn't be standing here today."

"And we also know that you didn't have your memory wiped. Skye leaked the information to us after the lab incident. Bad girl shenanigans, bloody brilliant!" Simmons smiled at him and extended her arm, "Thank you very much for the chance, Agent Ward!" She didn't expect the hug he'd pulled them both into.

"Time to go; we need to lead them a different direction considering our rendezvous point has been compromised. You should have sent a message and I'd have disarmed your trackers before you got here. Jemma, you're with me. Fitz, with Ward." She went to Ward's vehicle and picked up some weapons, and then she got into her vehicle and started it up as Jemma climbed into the passenger seat. Both girls knew something was off and they didn't like it. "Don't worry Jemma, extremely long range comms and an encrypted line. I need you to drive while I shut down your trackers."

They eased out of the parking lot and turned left, watching in the rear view mirror as the other vehicle went in the opposite direction.

Twenty minutes later, she spoke into the comm, "Grant, we have a tail... Keep going, it's time to teach them evasive maneuvers! Rendezvous point two is your target."

**Author's Note: My sincerest apologies for how long this has taken. It's now Tuesday, 01 July. My son's first birthday tomorrow and I've had no time for much, other than prepping for it. I've written as much as I can in between. This has to be the biggest chapter I've ever written and I'm not sure WTF I was thinking with it. Like, seriously! I don't have the slightest Scooby. I'm not even sure if it makes sense, but yeah. Let's go with it lol. If it doesn't make though, please let me know and I'll rewrite. Feedback is appreciated but as I've said before … Review, don't review. As The reader, that is your choice.**


	6. Chapter 6

_**Ghost Protocol**_

_Is a mess!_

**Disclaimer: I own nothing that is claimed by Marvel. **

**I do own a couple of later characters and this plot.**

**Author's Note: ****My sincerest apologies for taking so long. A lot has happened in the last month. China bombarding our servers, writers block, attempting to correct our sleeping pattern. Bleh! Alas, I have not forgotten about this, or my loyal readers. I've actually had most of this chapter written for a while and have just gotten done with the finishing touches. From the last line of this chapter, as you will see, there will be some bad language, etc. There will be a part of this that is dialogue only, due to comms of course. For that, Jemma is **_**italic. **_**Ward is bold. Fitz is ****underlined****. Enjoy!**

"So, you've seen some evasive manoeuvres, you need to drive from here on out. Just do as I said and we'll be fine!" Spotting a turn in, Skye pulled over. She dashed to the back seat pulled out one large black duffle bag after another, placing them in the bed of the truck. Simmons scooted over into the driver's seat, waiting until Skye opened each bag, loaded each weapon and was set to push on.

Skye nodded in Jemma's direction and pulled the phone out of her back pocket. Going through the encryption of both Simmons and Fitz' trackers with ease, she got them off-line within minutes.

Half an hour later and many miles up the road, they found themselves in the company of the very same black SUV. On seeing the vehicle, Simmons released the accelerator and hit the clutch, moved from third to fourth gear and floored it. After what seemed like forever of being unable to lose the SUV, Skye gave up.

"No evasion, let's see what they do!"

"Are you sure? You could get hurt?"

"Yeah, I might get hurt but I'll live. Besides, daddy Director would have my head on a silver platter if I left my gear on the Helicarrier!" The SUV sped up, but kept a safe distance. Skye raised her assault rifle and shouted, "Simmons, keep her steady." Flipping the setting to automatic, she took aimed and pulled the trigger. As she didn't intend to kill, she smirked as she seen the steam spout from the grill. The smirk dropped as another SUV pulled out from behind it and sped up until they were a couple of feet away from the bumper. She could clearly see the SHIELD insignia on the hood and sort of, kind of regret shooting the first vehicle. She picked up the large coin-looking thing, pushed the small activation button and launched. As it was designed specifically with vehicular targets in mind, the magnet stuck it to the vehicle; the driver lost control and veered to the side of the road.

It wouldn't damage the vehicle but if she had held onto it, it would have shut hers down. She hated shutting down SHIELD property and she hated that Coulson had sent them after her, but she loved working with the tech that Fitz had made, even though he was still trying to make this device smaller. Every time he made something new, he'd seek her out and pull the team, minus Ward, down to the testing area to watch. Sometimes they worked, sometimes he miscalculated and sometimes, but very rarely, the stuff didn't work.

When the SUV was gone from sight, she reloaded her weapons and sealed them back in their duffle. Speaking through comms, she told Ward and Fitz what happened. She turned to Jemma and stuck her head through the small window, "We need to double back, get a new car or we need a pick up. I wish we had the bus!" As she said the last word, their vehicle was hit from behind, "U-turn, now and don't stop driving, for anything until you reach Ward or the meeting point, whichever comes first. That's a direct order!" Skye braced herself, holding on to the side of the bed when Simmons pulled the handbrake and banked a hard left. The vehicle stopped dead for a few seconds while Jemma stumbled over the pedals and gears, and Skye took that as her cue to grab her ICER rifle and jump down. Sure, she loved the compact handgun sized ICER, but holding this weapon in her hands made her love Fitzsimmons all the more. It was neither heavy nor light, the perfect weight and she bathed in the feeling of the stock against her shoulder.

As the SUV that rammed them hadn't expected it, it took about a minute to realise what had happened and came to a screeching halt, reversing and turning. Jemma sped away as Skye made her way to the middle of the road. The SUV came to rest thirty feet from her. Standing with her feet shoulder width apart, she emptied the mag of the cartridges and laid them on the ground around her as they gathered their firearms and exited the vehicle.

Scanning her surroundings, she noticed Barton off to the far right, bow and ICER arrow ready. She kept the mask up and let the wind start, centred around him. He tried to release the arrow and almost tumbled out of the tree.

She focused on the agents directly in front of her. "He sent the goon squad? Really?" her expression showed the confusion rolling around in her brain. "He actually sent the GOON squad? _And_ Strike-Team-Delta!"

She could feel Natasha's presence behind her. She could see the fear in the eyes of those before her, the bobs of their adams apples as they swallowed, the shaking of their hands as weapons pointed at her. They knew this wouldn't go well. This wouldn't go well at all!

"You are in direct violation of protocol seven eight three two six, ma'am. We have been sent to bring you in," the agent was looking everywhere, but at her. When his eyes finally rested on her, he realised his mistake. He'd called her 'ma'am' and she wasn't happy.

"Agent Lee, may I remind you that you and your men are in direct violation of every sane protocol there is? Director's orders or not, _Ghost Protocol_ has been initiated and you are endangering the lives of fellow SHIELD agents by standing here. Never mind the fact that you almost gave that driver a heart attack. _Ghost Protocol,_ as I understand it, is a highly classified, no contact, don't-even-bother-looking protocol." as her voice volume and anger levels were rising, the colour of her eyes were changing, the wind was picking up everywhere, the agents in front of her were visibly shaken, and she hadn't let herself go..._yet!_

"Stand down, Deputy Director!" and that did it. Hovering a few inches above the road, the blackness sprinted up her veins, through every visible part of her body, the crimson of her eyes, she let go. Her face contorted into a sneer, her hair flapping wild and free in the wind. Leaving the SUV where it was, she lifted her hands, palms up and sent the ICER rounds home.

As she lulled the agents back to the ground, she ran towards them, pulling them to the side of the road. She left them with one weapon, no radio and no vehicle.

Tapping her comms, she spoke, "He sent the GOON squad, the freaking GOON squad! _And _Strike-Team-Delta! Can you believe that?"

_"He really sent the GOON squad? Strike-Team-Delta is understandable but the GOON squad?" _

**"Of course he did, the very best for the Deputy Director!"**

"I'm starting to think this is a bad idea, Skye."

"What? No! I need to go through with this. Y'all can go back if you want but I have to see this through. Jemma, how far away from your u-turn are you?"

_"Hmmm...coming up on the tenth mile now. Pulling over to wait for you and then you can have your precious pick-up back."_

She sighed and thought for a few minutes, "No, Jemz! I told you not to stop. Drive at the speed limit and meet up with Ward and Fitz. You two had better wait for her, if she gets hurt, so help me, you'll be spending the rest of your lives in Antarctica. Direct order! Disobey it, and I'll make you teach the cadets of opposing academies for a month!" She took a breath, "and besides, Barton and Romanoff are still giving chase. I can feel them! Barton wasn't close enough for a deep sleep and no doubt he'll wake Nat up. Get to the rendezvous point and ask for Meli. She'll know what's happened."

Passing the EMP'd SUV, she stomped the brakes. Relieving the agents of their weapons, she got back in her vehicle and drove off. When she felt she was at a safe enough distance, she pulled far into another side road.

Another text was sent, this time to Meli.

_Got three inbound. Keep them close, don't let any harm come to them. I have business with the Director to attend and I'm not happy! Will be in touch as soon as I can, RP3 protocol_

She could trust Meli with Fitzsimmons, and Ward, but she knew that the others within _G__host Protocol _wouldn't take to three newbies kindly_. _

Tapping her comms again, she informed the team that she'd be going dark for a while due to unforeseen circumstances. A quinjet had landed no too far from her position. Even if they could trace the signal, which she highly doubted, without her expertise anyway, they still wouldn't find the others.

Putting the other bud in her ear, she activated the comm link.

"Meli! Director's sent half the agency looking for me. Keep your head down, take charge and tell everyone that I'll kill them in the most imaginative ways possible if anything happens to the other three. "

"Are you sure this is a good idea, Dee-Dee?"

"Dee-Dee? I like it! Much better than Death Demon. Sending the coordinates now. Get everyone there, the place is already stocked and tell Billy that if he so much as hints at the lie detector, I'll put him in the field! I'll contact you as soon as I can."

She disabled the tracker and once again, let it all out as the wind carried her above the trees. One could say that she was flying, but that wasn't it. Not really. Iron Man, that was flying, against the wind in any which way he liked. Thor, that was flying with the use of Mjölnir and he could cross the universe just to get to Earth. This, this wasn't flying.

She touched down just as the last of the agents had disembarked the quinjet and made her way to a seat. Noticing the looks they gave her, "What? He's not going to leave me alone and I'm sick and tired of putting agents to sleep because of it. Get this bird in the air in the next two minutes; I have a temper to control!" She buckled herself in and watched as they scurried around, two to the pilot area and the rest to their seats.

When they landed on the Helicarrier, no-one was there to greet her. Probably thanks to the warning the pilot gave to whoever was on the other side. As she stepped off the plane, the other agents surrounded her in a tight box formation and led her inside.

The agents inside realised what was going on pretty quickly and seen the completely unmasked look of rage on her face, they plastered themselves to the walls. The anger had gone from simmering, to boiling as soon as they stepped through the doors.

"Step out, now!" They didn't move and her patience crumbled. "I said step out, NOW!" An unseen force pushed them away and there was no hint of wind. It was new to her but she hid the surprise because she was livid. The agents followed behind her as she made her way to the observation deck. "Director's gonna regret this!" someone grumbled and she turned on him.

"You have just been reassigned to Sci-Tech training as of now." The look on his face would have made her laugh if she hadn't caught Coulson in her peripheral. She pocket-dialled a number and stared the man in front of her down until he nodded and stepped back.

She waited, expecting A.C's explanation but all he asked was where his GOON squad and Strike-Tea-Delta were.

She screeched at him, "Are you in-fucking-sane?!"

**AN;**** As I've said before ... Review, don't review. As the reader, that choice is yours. **


	7. Chapter 7

_**Ghost Protocol**_

_Is a royal fucking mess!_

**Disclaimer: I own nothing that is claimed by Marvel. **

**I do own a couple of later characters and this plot**

_**AN;**__** Writing as fast as I possibly can. I was gonna attempt this is Skye's POV, but I've decided against it. I haven't done POV's in a LOOOOOOOONG time. Back to the story, enjoy!**_

Helicarrier Observation deck, undisclosed location.

The anger had gone from simmering to well above boiling point. That white-hot-poker rage was so very close to bursting through. Watching the Director flinch at what she was saying dampened it, a miniscule amount, "What were you thinking? You could have gotten us killed. You've put my lot in unnecessary danger! Violation of protocol seven eight three two six? That protocol doesn't exist and I know that because I helped you write the fucking protocol. You and you're band of merry fucking men are in direct violation of every sane protocol there has ever been! The Intel for this particular case is from a very well respected and reliable source. If we didn't plan it out properly, I wouldn't have activated the fucking protocol to begin with! _Ghost Protocol _has its own fucking protocols in place for this specific fucking reason and you, as Director, have violated every fucking one of them. Putting fellow agents at risk is unacceptable and you should think yourself lucky that I haven't called Fury; he'd have your ass for this! I asked you to trust me and you've violated that as well! It is a covert op, _MY_ covert op!" Throwing her hands in the air, she almost punched him, which would have been very bad for him.

He took her brief silence and jumped in, "Can we move this to a more private area, like my office?" She knew that she was well above and beyond anything they'd ever seen. She could tell why everyone looked so terrified, her file was well above their clearance levels, but they'd heard the stories. She couldn't exactly tell why they were staring at her eyes though. The hacktivist knew they turned red, but she'd never seen the sheer fear on Coulson's face, and she knew that he didn't want anyone else suffering when he was solely responsible for this major fuck-up! This was a new side of her that no-one had seen or expected. He knew she was fiercely protective and loyal, but this was _her_ operation and she hated it when he overstepped the line. As Deputy Director, she doesn't have to run everything by him, but he thought they had an understanding. She wouldn't do anything that was rash and improperly planned, and she never has. Ok, but that was one time. And Quinn was an arrogant, top class asshole! The despicable wanker put two in her abdomen. A.C should have let her die, if he did then none of what happened would have.

"No! I've been with you and SHIELD for a long time now and I thought we were past the stage of mistrust. But, it's a bit obvious that that's not the case." She turned slowly, catching the eyes of every person in the room, including those that weren't easily seen, finally landing back on him. "Everyone listen up!"

May stepped into the room and shouted, "Commander on deck!" None of them had ever seen people shuffling, if that's what you want to call it, about like that. Yeah, they'd seen military movies and all that jazz, but never in their lives had they ever seen veteran SHIELD agents act like a bunch of new recruits.

Skye gave the older woman an appreciative nod and faced the music, "All eyes on me! _Ghost Protocol_ is used for highly sensitive and classified operations. It is used in the most dangerous of cases. It is a 'don't-even-think-about-searching-for-them' protocol and I am warning each and every fucking one of you! If I ever, _ever, _have to go through this again- that is, putting my team in unnecessary situations- I will not hesitate to put each and every agent that comes after me down for good. Sleep will not be an option!" She hated threatening and despised killing, but she'd do whatever she deemed necessary against those intent on bringing harm to her charges, whether it be direct or indirect.

The young woman glared right into his eyes, never breaking the contact. "And I am telling you, here and fucking now, I programmed your systems, from the ground up. I am the only person in the fucking world that can take you down because of it and I will not take this kind of mistrust lightly. Director Coulson? Come looking for me one more time and you will regret kidnapping me from my van more than _anything. _Now, I have a team on the ground, more than likely dead thanks to you, but awaiting instruction and I'm taking that quinjet with me. Don't bother looking; I've disabled every possible way of tracking it." She marched away, and she was pretty proud of herself. She kept her temper and abilities in check, no wind, no unavoidable and unnecessary deaths, nothing of the sort. But, at the same time, she hated myself. She loved SHIELD and loved working with Coulson and the rest, but that was the last straw. Every covert operation she'd been a part of, he had to go and mess it up 'for her own protection'.

So yeah, she's Deputy Director and everyone respects her and blah, blah, blah! _I'm not some China doll and I'm not fragile._ Does she have a tattoo on her forehead that states otherwise? Hell no! She's grateful and she really does appreciate his fatherly tendencies but seriously, what's the deal? Training with the famous Black Widow and the damn Cavalry, it doesn't leave you defenceless. If anything, it's a deadly combination, especially when your genetics are like hers! _Don't get me wrong, my genetics aren't anything to be proud of, they're dangerous and I get that. But it's not as if I've gone over to the dark side, I'm no Anakin Skywalker. _

The Director just stood there, speechless. His mouth opening and closing like a fish. May stepped into his line of sight and sighed, "You know that's the biggest mistake you've ever made. Not only is she powerful due to her heritage, she's still gaining some of her abilities and you've just seen the darkest part of her, so far." She clicked her tongue, "She's never threatened to put anyone down but she will kill to protect those under her. Don't be stupid Phil, she can and she will take the organisation down if you force her hand."

He covered his face with both hands and rubbed his eyes hard, "I know, and yes, I know that she's not made of glass! But it's not a strategic play and how do we even know that she's prepared properly for this?"

Why couldn't she see that it was for her own good? Why did it feel as if he had a teenage daughter telling him not to bother messing up her date? Why wasn't May agreeing with him? Why was he the only one concerned with her safety? Why did running an organisation have to be this difficult? Especially with an out-of-the-box deputy?

He turned to a security specialist, "Lock the place down, nobody gets in, nobody gets out."

All eyes were on Phil as May forcefully grabbed his shirt and pulled him within an inch of her face, "Listen here and listen good! You have just put everyone on this Helicarrier at risk. Do you know what she's going to do when the klaxon blares and the screens squeal the lockdown protocol?" She took a breath, "She's going to come in here, she's going to put everyone to sleep and then, she's going to kill every single one of them to get her point across!" She shouted at everyone, "Get out of here, now!" People started scrambling, heading away from the exit Skye had used. They all wanted to be anywhere but there, anywhere but the position the Director had put himself in.

But she just kept on walking and ignored the panicked looks of those who crossed and rushed from her path, until she found her way to the deck. Of course, the klaxons were blaring, red lights flashing and the computer was on repeat. She slipped the phone out of her pocket and a whole ten seconds later, it all shut off and the door opened to reveal none other than Natasha and Clint. Both acknowledged her with a slight nod of the head, wary. They'd noticed her eyes were black and to them, it didn't seem out of character except for the fact that she was completely calm. Well, her demeanour and facial expression were calm, but inside, the rage was beginning to boil again.

"Tweety, you're piloting my ride. Ninja, please make sure I didn't give Coulson a heart attack?" Natasha gave both a smirk and sauntered off.

Clint placed his tongue between his teeth and gave his best Sylvester impression, "Awww! Sufferin' succotash!" He gave a loud belly laugh and proceeded to the quinjet. Taking up the pilot seat, he faced her when she spoke, "C.B? You tell anyone where you're taking me and I'll make Tasha look like a kitten!" A slight dip of the chin and he was back to pre-flight checks. Within five minutes, they were in the air at the extreme frustration of flight command.

She wouldn't hurt him, unless he pushed her too far and they both knew it. On the way to their co-ordinates, she explained what'd happened with the Director, how she was angry at herself and proud and all the weird emotions she was feeling. He explained why everyone, specialist or not, was terrified. He also explained that the reasons Strike-Team-Delta had gone to retrieve her. They knew here, they wouldn't use force unless absolutely necessary. However, had the GOON squad actually tried to force her to do anything, Clint and Nat would've taken them out and not in a very friendly way. Of course, Strike-Team-Delta was the best of the best and the next best was Coulson's old team then it was the GOON squad. Everyone disliked them, with the exception of Agent Antione Triplett. He was probably the only one of the fifteen that anyone actually liked. She couldn't remember seeing him on the road, but then again, he was probably running back end from elsewhere.

They passed the time, which wasn't as long as either would've liked, catching up. It'd been ages, to them, since their last meet and greet, and if she was being honest, she'd have loved to have taken them both with her. Duty calls though, so no such luck! She put both comms devices in her ears and channelled an open link with everyone on the ground.

"Ladies and gentlemen, prepare to be amazed as the one and only, Hawkeye, finally let's me outta this damn plane. Step back, climb trees, enjoy the show!" They passed over the road once, twice, three times until Hawk had deemed it safe enough. He dropped the ramp and turned to watch her do her thing, keeping the plane steady, "Remember Birdie, Nat will look like a kitten!" And with that, she launched herself out of the plane. Landing softer than she should have done, thanks to said genetics, she scrambled into the trees and waited until the plane was long gone before calling out.

_Ghost Protocol, is officially a go!_

_**AN; **__**Review, don't review. Your choice! Although, I'd really appreciate constructive criticism. I don't write to please anyone but myself tbh, but if my writing sucks, I'd like to know where I can improve. Thanks **_____


	8. Chapter 8

_**Ghost Protocol**_

_Is a royal fucking mess!_

**Disclaimer: I own nothing that is claimed by Marvel. **

**I do own a couple of later characters and this plot.**

_**AN; **__**PLEASE! READ THE NOTE AT THE BOTTOM BEFORE EXITING THE PAGE, THANK YOU!**_

_**Onwards and upwards, story time. Enjoy!**_

2 Months later. Undisclosed hostile location.

They'd had no problems with the Director since that day on the Helicarrier. Fury had visited and told him to back off, but demanded specific supplies.

It'd been a week since Skye had been captured. It was her intent. They'd spent over a month gathering Intel, developing weapons and catching up with their target and just like Quinn, she wasn't going to let them get away. She was tied to a chair in a dark cell, if you could call it that. It felt more like a closet, small and cramped. A small, almost burnt out bulb above her gave her no comfort. She'd be extremely comfortable in total darkness. She could feel the darkness creeping up, making her stronger and because of it, she disappeared into her thoughts.

_The others, collectively, rivalled her rage that day. The day she decided she was going in._

"_You're not going in alone. We're a team and we do things _together_, Deputy Director or not!" Ward folded his arms, feet shoulder width apart and tried to stare her down with the others following suit. She wasn't having it! She was an adult, a very capable female SHIELD agent and she'd be damned if anyone stopped her from her mission._

"_I am doing this, and I will be captured. I have the trackers in my teeth and other places. I have the vitals tracker in my tongue and I've already decrypted them for Fitz to get a read and follow me. If anything, I just want to see the look of the interrogators face when I laugh at him after he shoots me in the knee, point blank." She held her expression, calm and collected and watched as their eyes widened and jaws dropped._

"_What in the hell are you talking about? You're definitely not going in there alone and you are not getting caught. I'll call Fury, Coulson, Widow, Hawk, Cavalry, Tripp, anyone! You're not doing this." Simmons was hysterical and not the good kind. The deputy would have laughed if it weren't for the fact that she'd felt that very same concern when Jemma had almost killed herself, a couple of times now. _

_Oh, but Skye was definitely going in there and she'd definitely get captured, and she'd definitely be laughing at whoever tried to hurt her... But she'd just have to make sure they'd be sleeping when she set the plan in motion! Either that or she'd have to sedate them all. It was the only way and they weren't going to like it one tiny little bit. _

_They'd all been fitted with untraceable new trackers, specifically designed so that no-one with the exception of Skye and Fitz could find them. There'd been fifteen of them to begin with. Skye, Fitz, Simmons and Ward along with eleven others. In the beginning, there was only supposed to be twelve but with Ward's strategic planning and Fitzsimmons gadgets, she couldn't refuse them._

The sound of a key turning in the lock brought her from her thoughts. When the door swung open, she could make out the silhouette of her 'interrogator.' He stepped into the room and closed the door behind him. "You know the drill Death Demon! Tell us what we want to know and you won't have to suffer any more." She could see the small glint of light dancing around his unbelievably white teeth as he openly smiled at her. Deep down, he hated that he hadn't broken her. He hated that he couldn't get through to her, and he hated that he couldn't actually hurt her.

"Aw, is this the time we actually get to the really interrogating?" She was genuinely excited about this, in a very unnatural and unnerving way. It made his skin crawl. "Please, don't bother with the easy way! That's boring and quite insulting. If anything, I think you should just give up your secrets now, because when I can be bothered getting out of this chair, I'll show you what a real interrogation is." Seeing the look on his face, the pale and terrified look, she grinned. Skye spoke slowly and drawled it out, "Aw! Is the baby scared? Doesn't the baby like that idea? You've tried pretty much everything on me in a week! A week! Psychological interrogation techniques don't work, water-boarding doesn't work. Depriving me of pretty much everything doesn't work, the attempted rapes haven't worked. If you haven't realised, I'm pretty much a fearless bastard. I'm not suffering; I'm right in my element." She saw his left arm disappear behind his back, producing a handgun. "Oh!" she dragged the word out, "Is that a Desert Eagle Mark XIX, calibre .50AE?"

The guy just looked at her, mildly surprised. He stalked towards her, placed the barrel against her left thigh, "Last chance Demon. Tell me what I want to know and I won't pull the trigger!" He watched as she let her head fall, chin on her chest. What he didn't see, was the shit-eating grin that kidnapped her lips. When she finally raised her head, she heard him swallow.

"Do it!" Her smile got impossibly wider, "I dare you!" He pulled the trigger, point blank. "Ahhhhhh! Ha!" She buckled, laughing in his face. There was no blood, just a crumpled bullet sitting in a slight indenture of her thigh. "You see, Mr. Interrogator, Sir. You can't do a damn thing to me. Now, I'm tired of this horse shit!" She lifted her arms and straightened her legs, fast and hard, breaking the plastic ties. She stood up and circled him, effectively checking and creeping him out, "Sit!"

He done as he was told, against his will. He tried running away, he tried veering off course, but his body wouldn't let him. This ability was much like Lorelei, the Asgardian bitch that tried taking over the world but didn't get very far, TWICE. She escaped Asgard about two years after sexually assaulting Ward, no-one knows the how or why, but she did. Thankfully Skye and Lady Sif were able to apprehend her and send her back to Asgard, permanently.

"Breathe! I'm not going to kill you, yet. But while we're here, why don't I show you how a real interrogation is done?"

**AN;**** PLEASE READ THIS!**

**So, this was kinda rushed because I didn't wanna keep you guys waiting ages. I'm not entirely sure that this isn't boring all of y'all. Review, don't review. As the reader, that is your choice.**

**BUT! And that's a big but, I have been working on a crossover. AoS and another fandom. However, I'd like to know if anyone would be interested in it. If so, give me a little PM to let me know. I don't wanna post it and have no-one read it. The crossover is an experiment of sorts, I haven't done one before and it's my first fic for the other fandom. How many of y'all like Pacific Rim? Why wouldn't SHIELD be involved at some point? What, with the destruction of the breech and their knowledge of Extraterrestrial revenge?!**

**If you'd like to read the prologue before deciding on whether you'd like to read the fic then by all means, let me know and I'll see what I can do!**


	9. Chapter 9

**To Ghost Protocol's loyal readers, my sincerest apologies but this is NOT an update. **

**I can't concentrate on GP, at all. Believe me, I've tried so many times and I'm losing my sanity!**

**My mind is completely taken with Pacific Rim and the PR/AoS crossover idea. It's driving me mad!**

**I haven't been functioning properly because of it and I haven't posted anything yet.**

**I'm hoping to have at least a few chapters down and completely finished before that happens.**

**I am NOT abandoning GP, at all. It's just a temporary hiatus until I get this annoyingly consuming idea down in black and white.**

**Please, bear with me here! I'm pulling a complete blank with GP because Jaeger Bombs, as I've currently named it, is taking up everything I have.**

**My apologies again!**


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